Are you still wanting to use Skype now? Even after this sorry tale has surfaced, telling of Microsoft cuddling up to the Homeland Security department and putting a legal back-door in Skype allowing the government to listen to all voice traffic through the Skype system. You should never use Skype for anything that requires secrecy anyway, the conventional land-line telephone is probably more secure and reliable anyway, not to forget that judging by my experiences with people calling me on my mobile from Skype, the quality of the call can be very bad and it is hard to make out what the person is saying sometimes. The Skype calls will be directed in a way that includes a recording agent that will be able to record calls from terrorists and criminals online, but I guess this will keep us safe from terrorists and if Al Queda want to use Skype then they must know that they will be monitored and recorded. This will help cut down on crime in the United States and abroad, making us all safer, just be careful what you say on-line in future.
This makes you wonder if there are any back-doors in Windows we do not know about, I guess there would be since the security of Windows leaves a lot to be desired. It would be better to find an Open Source program that can do the task of Voice Over IP instead of using the closed source Skype program. GNU Free Call is a good alternative that looks very promising. And it is open source which would allow greater security. And if it is less bloated than the Skype application then everyone will win. it is obvious that any communication technology would be engineered to have security holes, the OpenBSD operating system; the most secure operating system available allegedly has security back-doors installed, this is only a rumour and considering the complexity of the code in question, finding the back-door code would not be easy at all.
The Windows operating system certainly would have back-doors installed to allow remote monitoring of user activity. The only really secure operating system would be one you had coded yourself so that all of the code had been vetted by you and there was no code in it where you did not understand the whole function. Of course this would be a massive undertaking, but it is not impossible, just very time-consuming to say the least to program an entire operating system from scratch. Therefore when using an OS that other people have worked on, you have to trust them that it is secure and safe to use. The same with the Skype software. The source is not available so you have to assume it is safe to use.